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During a routine re-staffing of Dragon Island, an old Soviet weapons installation in the Arctic, the replacement base crew comes under fire from an unknown enemy. Vasily Ivanov, a researcher assigned to manage Dragon and the crew's pilot, manages to send out a distress call and attempts to take off, however his plane is shot down.

Ivanov's distress call is intercepted by an American listening station in Alaska, and soon the American President and the heads of America's security agencies are briefed on Dragon Island; it was once the cornerstone of Soviet weapons research, a place where cutting-edge weapons were designed by scientists with a blank cheque. It has now been seized by an organisation calling themselves the "Army of Thieves", led by the enigmatic Lord of Anarchy. Self-proclaimed anarchists who have been garnering a reputation over the last several months, the Army is made up of enforcers of the Pinochet regime, Sudanese Janjaweed militants, Islamic fundamentalists and narco-terrorists. They are planning to unleash Dragon Island's centerpiece, known as the Tesla weapon. Experiments with rocket fuel and samples of acids acquired from the atmosphere of Venus have created a compound that, when ignited, can set fire to the atmosphere and cause untold damage to any nation caught in its blast. The Army of Thieves has been leaking the gas into the jet-stream above Dragon Island for several weeks, and most of the northern hemisphere is now contaminated. The Russians launch a nuclear missile to destroy their own island, only for the Army to divert it back at its silo. Following this, the Americans are asked if they have any teams nearby who might be able to stop the Army of Thieves.

At this time, USMC Captain Shane "Scarecrow" Schofield, has been reassigned to a small equipment-testing project in the Arctic. Although Schofield has been cleared for active duty (following his temporary leave of absence after the traumatic death of his girlfriend Elizabeth Gant), Schofield has been seen as a liability by the Corps, and has spent most of his time teaching new recruits. His situation has been further complicated by an outstanding bounty on his head; although members of the Majestic-12 conspiracy are dead, the French government has offered to pay the bounty as retaliation for his previous actions against them. Thus, to keep him out of harm's way, Schofield has been assigned to this research team. Also on the team are the Marines Mother, Billy "the Kid" Thompson and Vittorio "Mario" Puzo, a DARPA scientist named Zack Weinberg, and civilian contractors Emma Dawson, Jeff Hartigan and Chad. Also with them is Zack's prototype BRTE-500 (aka "Bertie", a mutli-functional, independently-intelligent robot). During the seven-week stay in the Arctic, Schofield has learned that a French DGSE agent known as Renard has requested to take up the mission to eliminate him.

Schofield's team is one of just two units close to Dragon Island; the other is a Navy SEAL team stationed on the USS Miami, a Los Angeles-class submarine. Ira "Ironbark" Barker, the leader of this unit, warns Schofield to stay away from Dragon Island or else risk being caught in the crossfire. Schofield decides to check out Ivanov's crashed plane, and then asks the civilian on the team to help him and his Marines shut down the Tesla device. While Zack, Emma and Chad agree, Hartigan believes it is a fool's mission and decides to remain at the team's camp.

Using their prototype Advanced Force Delivery Vehicles, Schofield's team navigates the ice leads to the crashed Beriev, where Ivanov is found to still be alive. As Schofield and Mother extract him, the SEAL team's insertion onto Dragon via an old submarine dock is a disaster, with every member of the team being killed off by the Army. As he realises they are being watched by a UAV, the Army then attacks Schofield's team with a pair of AH-1 Cobras and a V-22 Osprey, forcing Schofield, Mother and Ivanov back into the water. The situation is complicated by the arrival of a French submarine; Renard and a team of troopers have been tracking Schofield and are sending people to the surface to take him out. Fortunately the Army's choppers identify the submarine as a more dangerous threat and destroys it.

Considering the threat posed by the Army, Schofield decides to save Renard and two members of the French commando team sent after him, and they flee through the leads a partially-sunken research facility on an islet near Dragon. Momentarily safe, Renard identifies herself as Veronique Champion, cousin to Luc Champion (a French scientist killed in Ice Station), whom she believes Schofield to have killed during the events that took place at Wilkes. Schofield corrects the misassumption and then informs her of the Army's intent (which would also impact France) and so Champion agrees to help the Marine, but because of the other actions he has taken against France, Champion warns Schofield that she will still kill him once the threat is resolved.

Meanwhile, Hartigan is captured by a second Osprey (which he mistakenly believed to be a friendly), and the first Osprey returns to Dragon Island, so that the Army officer in charge of the attack, Hammerhead, can give his report to the Lord of Anarchy. In spite of the unexpected interference of the French submarine, the Lord of Anarchy is displeased with Hammerhead's failure, and so, to serve as a warning not to fail again, orders Hammerhead's second-in-command to cut off his own hand. After the gruesome act is carried out, the Army's First Officer, Typhon, informs the Lord of Anarchy that the red uranium spheres which are used to ignite the gas are over an hour away from being primed. Concerned by the determination of Schofield's testing team, the Lord of Anarchy orders Typhon to send in a team to attack them on the islet.

Now allied with the French commanods, Mother begins talking with one of them, Jean-Claude Francois Michel Huguenot, or Baba. During their conversation, Mother comes to believe that Baba is her match (based on what she read in a magazine horoscope) and realises she is attracted to him despite her now rocky marriage to Ralph.

Schofield and Champion question Ivanov on the facility, and how they might shut down the Tesla device. The Russian scientist suspects that the leader of the base's previous crew, Igor Kotsky, is the one who allowed the Army to take control of the island and will be priming the six spheres of red uranium for use; there is another sphere, but Ivanov believes that because Kotsky does not know of its existence, the Lord of Anarchy cannot either. In order to ignite the weapon, the Army needs to seed the atmosphere with the acid-rocket fuel mixture, before firing a battery of missiles armed with the red uranium spheres into the cloud. Given that it is too late for them to shut down the gas, and since that any missile-launching devices will be heavily guarded, Schofield decides that their best option is to target the red uranium and dump the spheres into the Arctic Ocean. When Mother questions why the Russians would build such a weapon, Ivanov reveals that the original plans for the Tesla device were stolen from the Americans.

The group comes under attack from an assault squad led by Bad Willy, forcing them to begin to fight their way through the polar bear infested installation. Realising too late they they are being forced towards an assault squad (resulting in the death of the French trooper Dubois) they are forced to scatter through the trenches of the islet's stadium, but luckily Schofield manages to take out the enemies ahead of them. While finding their way back to the others, Zack and Emma realise they are being stalked by Bad Willy, and it is only thanks to Bertie being able to shoot the deviant's ear off that they are able to escape back to the others.

While making their way through the remaining islets, the team loses Chad during an attempt to fool their way past the Army of Thieves by having some of them wear the Army's uniforms. They soon arrive at a cable car that leads onto Dragon Island itself. As the cable car travels, the Lord of Anarchy begins speaking to Schofield via an earpiece the Marine wore as part of the disguise attempt. Having identified him from the island's surveillance footage and accessed his personnel file, the Lord of Anarchy begins taunting Schofield with the details of Gant's death. In addition, he mocks the also-listening Mother and Champion and tells Schofield he shouldn't trust the Kid or Mario because of their own liabilities. While perturbed by the Lord of Anarchy's words, Schofield believes the Army leader would not be doing this if he didn't think Schofield's team actually stood a chance at stopping him.

While this is happening, David Fairfax - Schofield's friend in the Defense Intelligence Agency - has been researching the Army and Dragon Island at Schofield's request. He meets with analyst Marianne Retter, who has been studying the Army since they first came to light, and they are both suspicious that an irregular army such as the Army of Thieves would be able to carry out a string of attacks against high-value targets to arm themselves. While Retter is preparing to go to a meeting to brief the President on the Army, Fairfax realises that her escort car is fake, and so the two DIA analysts flee from the purported special agents.

Once the cable car has reached Dragon Island, Schofield initiates a plan to retrieve the red uranium spheres, and during the chaos the team causes, Ivanov leaves to find them a plane with which they can escape, Mario and the Kid are dispatched to try and take out the primary missile battery in case they fail to get the spheres, and Bertie is hit by an RPG and blasted off the island's edge. Schofield has Mother and Baba assist him in launching a truck over a bridge gap and securing it in place with the French version of the Maghook, the Le Magneteux, affording the Marine the chance to reach the tower where the red uranium spheres are being kept. Schofield takes the now fully primed six spheres from Kotsky, and then secures himself before detonating an explosive at the base of the tower, causing it to fall over (killing Kotsky in the process).

The whole team (barring the Kid and Mario) rejoin Ivanov, who has prepared an Antonov An-12 for them. However, a pair of Strelas and an RPG-wielding Army trooper take out the Antonov's forward landing gear, preventing the plane from taking off. Faced with a stand-off with the Army of Thieves, the Lord of Anarchy sends out a few berserkers, telling Schofield he can easily wear them down to retake the spheres if he really needed them. To their horror, the Lord of Anarchy reveals that he has the primed seventh sphere (Ivanov cannot figure out how he learned of its existence), and successfully fires a missile armed with the red uranium into the atmosphere.

Luckily, the gas does not ignite, because Ironbark (who survived the assault against his team) was able to shut down the gas diffusion process long enough to create a safe zone. The Lord of Anarchy realises now he does need Schofield's spheres, and orders his men to move in. During the subsequent assault, Ivanov is killed, Baba is captured, Zack, Emma and Mother are forced to flee into the island's southern mountains with two of the spheres, and Champion is injured. After the Antonov ends up falling into the sea, Schofield manages to dispose of the other four spheres before he rescues Veronique and escapes on a raft through the leads around the island.

While hiding from their pursuers, Fairfax and Retter go over the information they have, and on a list of files Fairfax obtained regarding Dragon Island, Retter recognises the name Marius Calderon, who has come up in the course of her investigation into the Army of Thieves. Calderon, the CIA's foremost expert on psychological operations, wrote about the island before the Soviet Union built anything there, prompting Fairfax and Retter to open the file, entitled "Geographical Locations for Operation Dragonslayer".

While looking for a way back onto the island, Champion questions why Schofield would save her when she has already vowed to kill him, and he tells her that while her initial belief that that he killed Luc may have been wrong, her reason for wanting to avenge her cousin was proof that she has a fair sense of justice. Champion doesn't believe this to be true of herself, and reveals that after her husband was killed because of a woman informant she trusted, she choose to become an assassin to try and avoid feeling empathy ever again. In response, Schofield answers her query as to how he has coped with Gant's death, revealing that after seeing a few Corps-assigned therapists, he found a private psychologist named Brooke Ulacco, who taught him to deal with the horrific loss by learning how to seal his memories of Gant so that no one can use her against him.

Schofield then receives the Operation Dragonslayer file from Fairfax. Calderon predicted the rise of China as an economic superpower by 2010 as early as 1982, and that, with the CIA's approval, he came up with a plan to allow the Soviet Union discover the plans to the Tesla weapon. In reality, the acid-rocket fuel mix has largely been distributed by the jetstream over China, India and Europe; once it is ignited, these regions will be decimated, while the United States will be relatively unaffected and able to preserve its position as the world's only economic superpower. In order to pull this plan off, Calderon needed someone to claim responsibility for the attack, and so began building the Army of Thieves as a fake terrorist group (though the majority of its recruits are unaware of the reason for the Army's existence). With all this information, Schofield and Champion deduce that the Lord of Anarchy is Calderon in disguise.

Meanwhile, being tracked by the Army, Mother creates a diversion for Zack and Emma to get away, and as a result she is captured. Also, the Kid and Mario, believing they are the only ones left, attempt to sabotage the Army's missile battery. During the attempt, Mario is contacted by Calderon and offered to chance to live if he defects. His assignment to the equipment-testing team having been an unofficial punishment for allegedly supplying relatives in the Italian mafia with weapons, the amoral Marine agrees and shoots the Kid in the head.

Schofield and Champion find an old whaling village that grants access onto the island. While attempting to take out a patrol, Schofield ends up being captured by Typhon, and is quickly knocked out and taken away. Because of her injuries, Champion is unable to do anything to rescue him, and is forced to remain in hiding in the village.

Schofield awakens in the Dragon Island gasworks, which is now pumping the gas once again. Revealing to Calderon he knows his identity, Calderon notes he is aware that of Schofield's team, only Zack and Emma remain at large with the last two spheres, revealing Mario's betrayal and the imprisonment of Ironbark, Baba, Hartigan and Mother. In order to draw Zack and Emma out, Calderon has the captives killed brutally so that their screams will be broadcast across the island.

First is Ironbark, who is electrocuted, and then Hartigan, who has his head locked in a wooden box with hungry rats. Mother and Baba are treated to the latter torture and Schofield is non-fatally electrocuted, before Bad Willy reports that he has managed to track and capture Zack and Emma. The two civilians and the spheres they have are brought to the gasworks, and Calderon rewards Bad Willy by letting his keep Emma as his own property. With Mother and Baba having long-since stopped showing signs of life, Calderon believes that he has broken Schofield's spirit, then takes his signature sunglasses as a prize and has Schofield electrocuted.

Meanwhile, Fairfax and Retter decide that the best way they can avoid being killed by the CIA agents after them is to get Retter ti her meeting with the President. Finding the White House being watched, they crash their car into the gate so that they are taken into security custody. Because Retter is noted to have a meeting, Fairfax and Retter meet with the President, requesting the CIA's representative be excused so that they can share what they've learned.

However, before his body is dumped into a furnace, Bertie reappears and resuscitates Schofield with his built-in defibrillators. Though he had been thought to have been destroyed, Bertie ended up in the whaling village, and gives Schofield Champion's weapons, allowing him to fight back agains the Army. As Schofield opens fire on the Army, Calderon, Typhon, Big Jesus and Mario flee with the two spheres. Finding that Mother and Baba are in fact alive (having biten the heads off of the rats locked in with them), Schofield then frees Zack and mounts the damaged Bertie on his back to give him shoulder-mounted weapons before giving chase.

Calderon's missile battery is destroyed the Kid (who survived Mario's betrayal long enough to sabotage the battery), so he gives one sphere to Big Jesus with the order to fire the final missile from a megatrain while he moves on to prepare to carry a warhead armed with the last red uranium sphere into the gas cloud so that it will detonate in the middle of the combustible substance. As they realise that Zack has gone after Bad Willy and Emma, Schofield opts to go after Calderon while Mother and Baba go after the megatrain. Zack manages to save Emma after spraying TEB acid into Bad Willy's face. As Mother and Baba successfully sabotage the megatrain by disabling its brakes, Mother realises that she is happy with Ralph before the megatrain crashes into the sea.

With Bertie giving him cover fire as he drives, Schofield reaches Calderon's plane and manages to adhere himself to it with his magneteux as it flies away from the island. Schofield confronts Mario, who, having been removed from Bertie's ally-recognition software, is killed by the robot. Schofield then grapples with Typhon, forcing him out of the plane with him in Calderon's jeep (but using his maghook to keep from falling. After Calderon initiates the warhead's detonation, he escapes the plane by dropping into the ocean in a mini-submersible, but misses Schofield. Schofield manages to drop the warhead from the plane, which lands in the sea, and when it detonates, it creates an EMP that knocks out Calderon's mini-sub.

While the main crisis is averted, with Calderon having disabled the uplink that prevented the Russians from successful missile strikes before departure (having intended to allow the Russians to destroy the Army once he had no more use of them) the Russian government has authorised a missile strike on Dragon Island, unaware of Schofield's success. Schofield flies the plane back to Dragon Island and gathers Champion, Zack and Emma (Schofield is unable to get in touch with Mother and Baba), however the remnants of the Army have unwittingly destroyed the plane, forcing the group to seek cover in a bunker on one of the islets instead. The missile destroys Dragon Island, wiping out the remaining members of the Army of Thieves.

Schofield and his team are found alive and well several days later, having survived the blast, as did Mother and Baba (the latter having had his injuries tended to thanks to Mother remembering some details about some of the things Zack had beeen testing on the trip).

Schofield, his team, Fairfax and Retter are commended by the President for their actions, while Champion has convinced the French government to lift the bounty on Schofield since his actions saved France in addition to China and Russia. The CIA claims that Calderon's submarine has been recovered and that Calderon was found dead inside because of the mini-sub's life-support failing. At Ulacco and Mother's suggestion, and having come to terms with Gant's death (helped by remembering Ulacco's teachings while he was being tortured by Calderon to avoid being broken psychologically), Schofield goes on a date with Veronique. However, upon returning to the Marine barracks later, he finds his stolen glasses in his room, implying that Calderon is alive.

Though technically it is the fourth main installment in the Scarecrow Series, the novella Hell Island is chronologically the fourth story in the series.

A few references are made to Hell Island, such as when Ivanov notes the island the story was based on, but no further details are elaborated on, unlike the other previous stories in the Scarecrow Series.

Despite being released eight years following Scarecrow, it is suggested that Army of Thieves takes place within a couple of years after Scarecrow (and Hell Island), despite many real-life events and technological updates (as of 2011) being referenced, implying that the Scarecrow Series may exist within a floating timeline.

The later inclusion of Schofield in The Four Legendary Kingdoms of the Huntsman Series (where Schofield is noted to be aged 42 in the year 2016) makes this less likely and instead suggests that Scarecrow and the Army of Thieves is indeed intended to be set more than a few years after Scarecrow.